I see this behavior too in v2.0.5 (Windows 8.1) - and here's little more detail about what I'm seeing:
when I run Pencil from the Windows 8.x Start screen, it launches perfectly fine.
when I right-click on the Pencil icon in the Windows 8.x Start screen, it pins to the Windows taskbar with the correct icon. When I click on it to launch Pencil it does so correctly, but it displays in the Windows taskbar as a new Pencil icon (see attached screenshot double-icon.bmp).
when Pencil is already running, and I pin Pencil to my taskbar (by right-clicking its taskbar icon and choosing "Pin this program to taskbar") I see what the original reporter saw (the icon changes to the blue globe icon for xulrunner.exe and when you click on it to launch Pencil it instead displays the standard xulrunner usage message box - see attached screenshot xulrunner.bmp).
From mcas...@thecodegroup.co.za on June 18, 2013 09:33:30
When I pin Pencil to my taksbar in windows the icon changes from the Pencil icon to the xml runner icon
v2.0.3 Windows 8
Original issue: http://code.google.com/p/evoluspencil/issues/detail?id=571